Bridge edge loops gives weird results
This is far from ideal but it's a quick fix:



Extrude one of your edge loops and place it near or inside the other one.



Then bridge them.



Select the middle loop, hover over "smooth Vertex" and hold RETURN until it's stretched. 



Of course this creates more horrible geometry. It might be better to use a cylinder made of quads and use a Shrinkwrap Modifier to get an inner wall. Or use the Shrinkwrap to replace the original organic wall with one that has a nice topology.

Blender is not really equipped to handle a lot of chaotic tris. Quads make bridging and other operations much easier and more predictable. Ideally the vertex count of both loops should be the same and the verts should be evenly spaced.

A crazier way:

Hide everything except your edgeloops. if they line up on an axis, hover over the axis in the transform panel (Y in this example) and hit CTRLC



LMB drag the value up until the loops roughly align.



Bridge them.



Select the moved loop, hover over the Y axis and hit CTRLV. The loop will be back in its place.



Yet another way would be to bridge the hole piece by piece and not in one go.

I must admit that so far I haven't been able to recreate your troubles, so the solutions are a bit of guesswork.